Multiple sequence alignment - TraesCS7D01G500300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G500300 chr7D 100.000 5433 0 0 1 5433 606649009 606643577 0.000000e+00 10033
1 TraesCS7D01G500300 chr7A 91.684 4738 237 73 753 5433 698691105 698686468 0.000000e+00 6421
2 TraesCS7D01G500300 chr7B 89.864 4943 261 88 607 5433 690872027 690867209 0.000000e+00 6131
3 TraesCS7D01G500300 chr3D 92.190 589 39 4 1 587 11282994 11283577 0.000000e+00 826
4 TraesCS7D01G500300 chr2D 92.007 588 37 7 1 585 218779968 218780548 0.000000e+00 817
5 TraesCS7D01G500300 chr2D 91.525 590 42 5 1 587 186640318 186640902 0.000000e+00 806
6 TraesCS7D01G500300 chr2D 91.002 589 45 5 1 587 617901105 617901687 0.000000e+00 787
7 TraesCS7D01G500300 chr5B 91.851 589 41 4 1 587 7072054 7071471 0.000000e+00 815
8 TraesCS7D01G500300 chr1D 91.809 586 40 5 1 584 54940205 54939626 0.000000e+00 809
9 TraesCS7D01G500300 chr1D 91.216 592 44 5 1 590 411580537 411581122 0.000000e+00 798
10 TraesCS7D01G500300 chr5D 91.667 588 40 6 1 586 534089339 534089919 0.000000e+00 806
11 TraesCS7D01G500300 chr2B 91.186 590 42 7 1 587 507834563 507833981 0.000000e+00 793
12 TraesCS7D01G500300 chr6D 76.124 356 62 17 3344 3688 103003178 103003521 1.210000e-36 165
13 TraesCS7D01G500300 chr6B 76.803 319 58 15 3143 3451 188668024 188668336 1.210000e-36 165
14 TraesCS7D01G500300 chr6A 85.185 108 16 0 3344 3451 124267701 124267808 1.600000e-20 111


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G500300 chr7D 606643577 606649009 5432 True 10033 10033 100.000 1 5433 1 chr7D.!!$R1 5432
1 TraesCS7D01G500300 chr7A 698686468 698691105 4637 True 6421 6421 91.684 753 5433 1 chr7A.!!$R1 4680
2 TraesCS7D01G500300 chr7B 690867209 690872027 4818 True 6131 6131 89.864 607 5433 1 chr7B.!!$R1 4826
3 TraesCS7D01G500300 chr3D 11282994 11283577 583 False 826 826 92.190 1 587 1 chr3D.!!$F1 586
4 TraesCS7D01G500300 chr2D 218779968 218780548 580 False 817 817 92.007 1 585 1 chr2D.!!$F2 584
5 TraesCS7D01G500300 chr2D 186640318 186640902 584 False 806 806 91.525 1 587 1 chr2D.!!$F1 586
6 TraesCS7D01G500300 chr2D 617901105 617901687 582 False 787 787 91.002 1 587 1 chr2D.!!$F3 586
7 TraesCS7D01G500300 chr5B 7071471 7072054 583 True 815 815 91.851 1 587 1 chr5B.!!$R1 586
8 TraesCS7D01G500300 chr1D 54939626 54940205 579 True 809 809 91.809 1 584 1 chr1D.!!$R1 583
9 TraesCS7D01G500300 chr1D 411580537 411581122 585 False 798 798 91.216 1 590 1 chr1D.!!$F1 589
10 TraesCS7D01G500300 chr5D 534089339 534089919 580 False 806 806 91.667 1 586 1 chr5D.!!$F1 585
11 TraesCS7D01G500300 chr2B 507833981 507834563 582 True 793 793 91.186 1 587 1 chr2B.!!$R1 586

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
872 878 0.033504 GACTCAACTGCACCCGAGAA 59.966 55.000 8.17 0.0 0.0 2.87 F
873 879 0.034059 ACTCAACTGCACCCGAGAAG 59.966 55.000 8.17 0.0 0.0 2.85 F
1236 1274 0.041833 CTCCCCCTTCCAGTGAGAGA 59.958 60.000 0.00 0.0 0.0 3.10 F
1237 1275 0.041833 TCCCCCTTCCAGTGAGAGAG 59.958 60.000 0.00 0.0 0.0 3.20 F
1590 1662 0.588252 ATTTCTCTGCGTGTGTGTGC 59.412 50.000 0.00 0.0 0.0 4.57 F
2680 2783 1.136828 AGTGGTGTGGGTTCTTGCTA 58.863 50.000 0.00 0.0 0.0 3.49 F
3055 3160 2.629137 TCCCTACACTTTACTTCGCACA 59.371 45.455 0.00 0.0 0.0 4.57 F
4313 4427 0.902531 TACCTGTCCCTGCTGCTTAC 59.097 55.000 0.00 0.0 0.0 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2178 0.533755 ACTGCAACACACAGAGGAGC 60.534 55.000 0.00 0.00 38.55 4.70 R
2516 2619 1.352156 CCTTGTAGACGCAGCCGAAC 61.352 60.000 0.00 0.00 38.29 3.95 R
3125 3231 2.233676 CCCTGCCCAGTTTCAATTTACC 59.766 50.000 0.00 0.00 0.00 2.85 R
3280 3386 5.334879 GGTTACCTGCAGTCAACATGTAAAG 60.335 44.000 22.14 3.75 32.39 1.85 R
3508 3616 3.930634 AAGGAGAATTTTGCTGCTCAC 57.069 42.857 0.00 0.00 32.56 3.51 R
4147 4260 0.543410 TAACTCTGAGCGTTCCCCCA 60.543 55.000 4.19 0.00 0.00 4.96 R
4315 4429 0.667993 GGAGCTCTCACTCATCCTCG 59.332 60.000 14.64 0.00 38.50 4.63 R
5392 5562 0.947244 AGTGCAGCTACAGCAACAAC 59.053 50.000 3.70 0.00 44.64 3.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.073722 TCCTACGTGTGGTCTCCGT 59.926 57.895 0.00 0.00 38.53 4.69
72 73 1.813178 GCTGCTATGCATGCTCATGAT 59.187 47.619 20.33 5.95 41.20 2.45
75 76 1.743958 GCTATGCATGCTCATGATCCC 59.256 52.381 20.33 0.00 41.20 3.85
93 94 1.373497 CGTTCTGTTGAGGCGAGCT 60.373 57.895 0.00 0.00 0.00 4.09
110 111 1.893919 GCTTCGGGCTCTTGGTCTCT 61.894 60.000 0.00 0.00 38.06 3.10
175 176 3.865745 CCGACTTGCTAATCGTCTTGAAT 59.134 43.478 0.00 0.00 36.60 2.57
180 181 5.705441 ACTTGCTAATCGTCTTGAATTTCCA 59.295 36.000 0.00 0.00 0.00 3.53
218 219 1.235724 AGGTTCGTGTTAAGCTTGGC 58.764 50.000 9.86 1.97 33.54 4.52
219 220 0.948678 GGTTCGTGTTAAGCTTGGCA 59.051 50.000 9.86 4.89 0.00 4.92
220 221 1.334689 GGTTCGTGTTAAGCTTGGCAC 60.335 52.381 19.10 19.10 0.00 5.01
221 222 1.602377 GTTCGTGTTAAGCTTGGCACT 59.398 47.619 23.39 0.00 0.00 4.40
222 223 1.508632 TCGTGTTAAGCTTGGCACTC 58.491 50.000 23.39 12.51 0.00 3.51
223 224 1.202592 TCGTGTTAAGCTTGGCACTCA 60.203 47.619 23.39 13.01 0.00 3.41
236 237 2.229792 GGCACTCAGTTGATTGTGGAA 58.770 47.619 2.14 0.00 0.00 3.53
247 248 2.289882 TGATTGTGGAAGCTCCTCTGTG 60.290 50.000 0.00 0.00 37.46 3.66
263 265 4.932105 TGGTGCCCTGGGGTTTGC 62.932 66.667 16.03 0.00 37.65 3.68
339 341 1.101635 TCGACGCACCCCTCATCTAG 61.102 60.000 0.00 0.00 0.00 2.43
340 342 1.068250 GACGCACCCCTCATCTAGC 59.932 63.158 0.00 0.00 0.00 3.42
341 343 1.381872 ACGCACCCCTCATCTAGCT 60.382 57.895 0.00 0.00 0.00 3.32
342 344 0.106167 ACGCACCCCTCATCTAGCTA 60.106 55.000 0.00 0.00 0.00 3.32
358 360 2.458620 AGCTACCTGGTCCTGTTAGTC 58.541 52.381 0.63 0.00 0.00 2.59
615 621 7.011499 TGTAGATGCTCTAAGTGGGTAAAAA 57.989 36.000 0.00 0.00 29.58 1.94
617 623 8.764558 TGTAGATGCTCTAAGTGGGTAAAAATA 58.235 33.333 0.00 0.00 29.58 1.40
619 625 6.768381 AGATGCTCTAAGTGGGTAAAAATAGC 59.232 38.462 0.00 0.00 0.00 2.97
622 628 6.374333 TGCTCTAAGTGGGTAAAAATAGCTTG 59.626 38.462 0.00 0.00 0.00 4.01
623 629 6.598064 GCTCTAAGTGGGTAAAAATAGCTTGA 59.402 38.462 0.00 0.00 0.00 3.02
624 630 7.120726 GCTCTAAGTGGGTAAAAATAGCTTGAA 59.879 37.037 0.00 0.00 0.00 2.69
640 646 5.912892 AGCTTGAAGAGTATAAAGAGAGCC 58.087 41.667 0.00 0.00 0.00 4.70
641 647 5.053811 GCTTGAAGAGTATAAAGAGAGCCC 58.946 45.833 0.00 0.00 0.00 5.19
643 649 4.279145 TGAAGAGTATAAAGAGAGCCCGT 58.721 43.478 0.00 0.00 0.00 5.28
666 672 4.952957 TGGGGAAATTATTCGAAATGAGCA 59.047 37.500 0.00 0.00 36.36 4.26
670 676 7.428826 GGGAAATTATTCGAAATGAGCATTCT 58.571 34.615 0.00 0.00 36.36 2.40
671 677 7.592903 GGGAAATTATTCGAAATGAGCATTCTC 59.407 37.037 0.00 0.00 36.84 2.87
672 678 8.348507 GGAAATTATTCGAAATGAGCATTCTCT 58.651 33.333 0.00 0.00 37.05 3.10
673 679 9.727627 GAAATTATTCGAAATGAGCATTCTCTT 57.272 29.630 0.00 0.00 40.03 2.85
683 689 3.055530 TGAGCATTCTCTTTGAGGAGACC 60.056 47.826 0.00 0.00 41.39 3.85
684 690 2.093764 AGCATTCTCTTTGAGGAGACCG 60.094 50.000 0.00 0.00 41.39 4.79
687 693 1.546961 TCTCTTTGAGGAGACCGGAC 58.453 55.000 9.46 0.10 37.43 4.79
719 725 2.876079 GCCTCAGGAACGGATCTTGTTT 60.876 50.000 0.00 0.00 36.56 2.83
726 732 4.827284 AGGAACGGATCTTGTTTGTTTCAT 59.173 37.500 5.55 0.00 0.00 2.57
781 787 2.656973 CCAAACAAACGCACGCCC 60.657 61.111 0.00 0.00 0.00 6.13
856 862 1.197264 GAGCAACGTACTCACTCGACT 59.803 52.381 12.36 0.00 34.18 4.18
857 863 1.197264 AGCAACGTACTCACTCGACTC 59.803 52.381 0.00 0.00 0.00 3.36
868 874 1.734477 CTCGACTCAACTGCACCCG 60.734 63.158 0.00 0.00 0.00 5.28
871 877 1.666011 GACTCAACTGCACCCGAGA 59.334 57.895 8.17 0.00 0.00 4.04
872 878 0.033504 GACTCAACTGCACCCGAGAA 59.966 55.000 8.17 0.00 0.00 2.87
873 879 0.034059 ACTCAACTGCACCCGAGAAG 59.966 55.000 8.17 0.00 0.00 2.85
874 880 1.294659 CTCAACTGCACCCGAGAAGC 61.295 60.000 0.00 0.00 0.00 3.86
945 961 3.123621 GTCTCAAGTACTCAACGCCATTG 59.876 47.826 0.00 0.00 39.94 2.82
946 962 3.006430 TCTCAAGTACTCAACGCCATTGA 59.994 43.478 0.00 0.00 45.39 2.57
947 963 3.935203 CTCAAGTACTCAACGCCATTGAT 59.065 43.478 0.00 0.00 46.37 2.57
948 964 5.079689 TCAAGTACTCAACGCCATTGATA 57.920 39.130 0.00 0.00 46.37 2.15
949 965 5.483811 TCAAGTACTCAACGCCATTGATAA 58.516 37.500 0.00 0.00 46.37 1.75
981 997 3.307829 CGTGTACTACAGCCTCACG 57.692 57.895 0.00 0.00 43.77 4.35
1103 1137 2.829003 CGGCGAGGAGGAGTGCTA 60.829 66.667 0.00 0.00 0.00 3.49
1207 1242 4.404654 CAACGCCGCCAGCTTTCC 62.405 66.667 0.00 0.00 40.39 3.13
1224 1262 2.040278 CTGTGCTCTCCTCCCCCT 59.960 66.667 0.00 0.00 0.00 4.79
1225 1263 1.614824 CTGTGCTCTCCTCCCCCTT 60.615 63.158 0.00 0.00 0.00 3.95
1227 1265 2.041265 TGCTCTCCTCCCCCTTCC 59.959 66.667 0.00 0.00 0.00 3.46
1230 1268 1.394151 CTCTCCTCCCCCTTCCAGT 59.606 63.158 0.00 0.00 0.00 4.00
1231 1269 0.980231 CTCTCCTCCCCCTTCCAGTG 60.980 65.000 0.00 0.00 0.00 3.66
1232 1270 1.081092 CTCCTCCCCCTTCCAGTGA 59.919 63.158 0.00 0.00 0.00 3.41
1233 1271 0.980231 CTCCTCCCCCTTCCAGTGAG 60.980 65.000 0.00 0.00 0.00 3.51
1234 1272 1.081092 CCTCCCCCTTCCAGTGAGA 59.919 63.158 0.00 0.00 0.00 3.27
1235 1273 0.980231 CCTCCCCCTTCCAGTGAGAG 60.980 65.000 0.00 0.00 0.00 3.20
1236 1274 0.041833 CTCCCCCTTCCAGTGAGAGA 59.958 60.000 0.00 0.00 0.00 3.10
1237 1275 0.041833 TCCCCCTTCCAGTGAGAGAG 59.958 60.000 0.00 0.00 0.00 3.20
1238 1276 0.041833 CCCCCTTCCAGTGAGAGAGA 59.958 60.000 0.00 0.00 0.00 3.10
1239 1277 1.484038 CCCCTTCCAGTGAGAGAGAG 58.516 60.000 0.00 0.00 0.00 3.20
1240 1278 1.006519 CCCCTTCCAGTGAGAGAGAGA 59.993 57.143 0.00 0.00 0.00 3.10
1241 1279 2.378038 CCCTTCCAGTGAGAGAGAGAG 58.622 57.143 0.00 0.00 0.00 3.20
1242 1280 2.025416 CCCTTCCAGTGAGAGAGAGAGA 60.025 54.545 0.00 0.00 0.00 3.10
1243 1281 3.282021 CCTTCCAGTGAGAGAGAGAGAG 58.718 54.545 0.00 0.00 0.00 3.20
1244 1282 3.054434 CCTTCCAGTGAGAGAGAGAGAGA 60.054 52.174 0.00 0.00 0.00 3.10
1245 1283 3.912496 TCCAGTGAGAGAGAGAGAGAG 57.088 52.381 0.00 0.00 0.00 3.20
1246 1284 3.449918 TCCAGTGAGAGAGAGAGAGAGA 58.550 50.000 0.00 0.00 0.00 3.10
1247 1285 3.452264 TCCAGTGAGAGAGAGAGAGAGAG 59.548 52.174 0.00 0.00 0.00 3.20
1248 1286 3.452264 CCAGTGAGAGAGAGAGAGAGAGA 59.548 52.174 0.00 0.00 0.00 3.10
1249 1287 4.442612 CCAGTGAGAGAGAGAGAGAGAGAG 60.443 54.167 0.00 0.00 0.00 3.20
1250 1288 4.403752 CAGTGAGAGAGAGAGAGAGAGAGA 59.596 50.000 0.00 0.00 0.00 3.10
1251 1289 4.648762 AGTGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1252 1290 4.646945 GTGAGAGAGAGAGAGAGAGAGAGA 59.353 50.000 0.00 0.00 0.00 3.10
1253 1291 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
1254 1292 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1255 1293 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1256 1294 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1257 1295 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1258 1296 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1259 1297 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1260 1298 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1261 1299 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1262 1300 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1276 1314 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1361 1403 2.515523 CTCCATTGCCGCTCCTGG 60.516 66.667 0.00 0.00 0.00 4.45
1542 1602 1.522569 CCGAGGGACCAGGATTCAC 59.477 63.158 0.00 0.00 0.00 3.18
1580 1652 6.429385 TCCTTTCTTCTTCTGAATTTCTCTGC 59.571 38.462 0.00 0.00 0.00 4.26
1590 1662 0.588252 ATTTCTCTGCGTGTGTGTGC 59.412 50.000 0.00 0.00 0.00 4.57
1594 1666 2.351097 CTGCGTGTGTGTGCGTTG 60.351 61.111 0.00 0.00 0.00 4.10
1642 1714 7.761704 TCATAACATCTAGCAAGTTCAGAGTTC 59.238 37.037 0.00 0.00 0.00 3.01
1663 1736 8.561738 AGTTCTTCCTCTGCGAATTTAATTTA 57.438 30.769 0.00 0.00 0.00 1.40
1676 1749 8.798153 GCGAATTTAATTTAGATTGGAACTGTG 58.202 33.333 6.05 0.00 0.00 3.66
1704 1777 7.095649 TGCATATCTCGGATCTTTGTAATTTCG 60.096 37.037 0.00 0.00 0.00 3.46
1707 1780 7.611213 ATCTCGGATCTTTGTAATTTCGTTT 57.389 32.000 0.00 0.00 0.00 3.60
1762 1843 5.357314 GCTAGTTTTCTACCTGGGGAATTTC 59.643 44.000 0.00 0.00 0.00 2.17
1795 1876 2.004583 TTATTCGACTTCTGTGGCCG 57.995 50.000 0.00 0.00 0.00 6.13
1875 1956 1.296056 CCCTTTAACGTCACTGCGGG 61.296 60.000 0.00 0.00 35.98 6.13
1880 1961 1.434555 TAACGTCACTGCGGGAATTG 58.565 50.000 0.00 0.00 35.98 2.32
1934 2015 6.534475 TTTTCCGTTAGAATCTACTGCCTA 57.466 37.500 0.00 0.00 33.44 3.93
1959 2040 6.554605 ACCCCAAAATTCAAATCTCTCTTCAA 59.445 34.615 0.00 0.00 0.00 2.69
2087 2178 2.945890 GCCCAGTTCCACCTAATTCCAG 60.946 54.545 0.00 0.00 0.00 3.86
2336 2436 1.140852 TGGGATGATTAAGCCAGACCG 59.859 52.381 0.00 0.00 0.00 4.79
2338 2438 2.421529 GGGATGATTAAGCCAGACCGTT 60.422 50.000 0.00 0.00 0.00 4.44
2370 2473 1.593196 ACATTGTTCAGACACCACCG 58.407 50.000 0.00 0.00 34.98 4.94
2606 2709 2.492090 CCGGACTGCGAGAAGGAG 59.508 66.667 0.00 0.00 44.60 3.69
2623 2726 2.632996 AGGAGTTCGAGGTGAATGTTGA 59.367 45.455 0.00 0.00 39.21 3.18
2680 2783 1.136828 AGTGGTGTGGGTTCTTGCTA 58.863 50.000 0.00 0.00 0.00 3.49
2751 2856 3.731728 GGCAGGATCAGGCACCCA 61.732 66.667 9.65 0.00 0.00 4.51
3055 3160 2.629137 TCCCTACACTTTACTTCGCACA 59.371 45.455 0.00 0.00 0.00 4.57
3065 3170 3.288308 CTTCGCACAGAGCCCGAGT 62.288 63.158 0.00 0.00 41.38 4.18
3081 3187 4.563976 GCCCGAGTGATGATTTTTCAATTG 59.436 41.667 0.00 0.00 0.00 2.32
3082 3188 5.713025 CCCGAGTGATGATTTTTCAATTGT 58.287 37.500 5.13 0.00 0.00 2.71
3093 3199 2.721274 TTCAATTGTTGTGCCGATGG 57.279 45.000 5.13 0.00 0.00 3.51
3104 3210 3.153024 GCCGATGGCTGTCTGTTTA 57.847 52.632 0.00 0.00 46.69 2.01
3114 3220 8.331022 CGATGGCTGTCTGTTTATATAATATGC 58.669 37.037 0.00 0.00 0.00 3.14
3115 3221 9.388506 GATGGCTGTCTGTTTATATAATATGCT 57.611 33.333 0.00 0.00 0.00 3.79
3116 3222 9.745018 ATGGCTGTCTGTTTATATAATATGCTT 57.255 29.630 0.00 0.00 0.00 3.91
3254 3360 4.020218 TCAATGCTAAGGTACACTGCTTCT 60.020 41.667 0.00 0.00 0.00 2.85
3736 3849 5.916883 GGCATCGAGTAATTCATTTGGATTG 59.083 40.000 0.00 0.00 0.00 2.67
3751 3864 5.471556 TTGGATTGCACAATTTGATCAGT 57.528 34.783 2.79 0.00 0.00 3.41
3752 3865 5.063180 TGGATTGCACAATTTGATCAGTC 57.937 39.130 2.79 6.52 0.00 3.51
3789 3902 7.721286 AACTAGTTCTCTTTCAGTGTTCATG 57.279 36.000 1.12 0.00 0.00 3.07
4147 4260 4.473520 CTGGTGCCCGCGGATCTT 62.474 66.667 30.73 0.00 0.00 2.40
4313 4427 0.902531 TACCTGTCCCTGCTGCTTAC 59.097 55.000 0.00 0.00 0.00 2.34
4315 4429 1.078143 CTGTCCCTGCTGCTTACCC 60.078 63.158 0.00 0.00 0.00 3.69
4440 4558 7.545615 AGAAACGAAAGCATTTTTCTTTTCTGT 59.454 29.630 22.37 9.00 46.15 3.41
4542 4660 1.754745 GACTCCACACAGGCCTCAA 59.245 57.895 0.00 0.00 37.29 3.02
4543 4661 0.603975 GACTCCACACAGGCCTCAAC 60.604 60.000 0.00 0.00 37.29 3.18
4544 4662 1.344953 ACTCCACACAGGCCTCAACA 61.345 55.000 0.00 0.00 37.29 3.33
4545 4663 0.604780 CTCCACACAGGCCTCAACAG 60.605 60.000 0.00 0.00 37.29 3.16
4546 4664 1.149174 CCACACAGGCCTCAACAGT 59.851 57.895 0.00 0.00 0.00 3.55
4547 4665 0.466189 CCACACAGGCCTCAACAGTT 60.466 55.000 0.00 0.00 0.00 3.16
4548 4666 0.664761 CACACAGGCCTCAACAGTTG 59.335 55.000 0.00 6.99 0.00 3.16
4549 4667 0.466189 ACACAGGCCTCAACAGTTGG 60.466 55.000 13.52 4.33 0.00 3.77
4550 4668 1.529244 ACAGGCCTCAACAGTTGGC 60.529 57.895 13.52 9.62 45.42 4.52
4592 4720 8.435430 TGCATACGAAATCTGATTATCGATTTC 58.565 33.333 26.36 24.85 45.96 2.17
4598 4727 7.786178 AAATCTGATTATCGATTTCGGACAA 57.214 32.000 17.15 0.27 35.55 3.18
4620 4749 2.859273 ATCGCAACGCTTCCTCCCAG 62.859 60.000 0.00 0.00 0.00 4.45
4632 4761 5.588648 CGCTTCCTCCCAGAAAACATAAATA 59.411 40.000 0.00 0.00 0.00 1.40
4643 4772 8.971321 CCAGAAAACATAAATATAATGCAGCAC 58.029 33.333 0.00 0.00 0.00 4.40
4660 4789 5.844301 CAGCACGTGCACATATTCATATA 57.156 39.130 39.21 0.00 45.16 0.86
4661 4790 5.850931 CAGCACGTGCACATATTCATATAG 58.149 41.667 39.21 9.31 45.16 1.31
4663 4792 4.436050 GCACGTGCACATATTCATATAGGC 60.436 45.833 34.52 0.33 41.59 3.93
4664 4793 4.690280 CACGTGCACATATTCATATAGGCA 59.310 41.667 18.64 0.00 32.25 4.75
4665 4794 4.931601 ACGTGCACATATTCATATAGGCAG 59.068 41.667 18.64 0.00 34.08 4.85
4715 4854 9.421806 TGGTTGCATTATTTTAAATTGACTGAG 57.578 29.630 0.00 0.00 0.00 3.35
4725 4864 8.523523 TTTTAAATTGACTGAGCATGAACATG 57.476 30.769 10.04 10.04 41.60 3.21
4726 4865 5.970317 AAATTGACTGAGCATGAACATGA 57.030 34.783 17.40 0.00 41.20 3.07
4727 4866 5.970317 AATTGACTGAGCATGAACATGAA 57.030 34.783 17.40 2.86 41.20 2.57
4728 4867 4.754372 TTGACTGAGCATGAACATGAAC 57.246 40.909 17.40 10.56 41.20 3.18
4731 4870 5.490159 TGACTGAGCATGAACATGAACATA 58.510 37.500 17.40 4.92 41.20 2.29
4734 4873 7.121611 TGACTGAGCATGAACATGAACATAAAT 59.878 33.333 17.40 4.31 41.20 1.40
4759 4898 6.889177 TCAGCCATGTATAATTTCACAAGGAA 59.111 34.615 14.24 1.09 35.94 3.36
4908 5053 0.476338 TTGCCCTGTGCTCAAGGTAA 59.524 50.000 3.17 3.17 42.00 2.85
4946 5092 3.059352 AGGTGGTCAGTAACATCAAGC 57.941 47.619 0.00 0.00 0.00 4.01
4985 5135 5.192927 CAGGGCAGTCAAGTAATTTCCATA 58.807 41.667 0.00 0.00 0.00 2.74
4989 5139 6.770785 GGGCAGTCAAGTAATTTCCATACATA 59.229 38.462 0.00 0.00 0.00 2.29
5021 5174 4.422073 TTACATGCCATCTAGAACCTGG 57.578 45.455 6.51 6.51 0.00 4.45
5022 5175 2.200081 ACATGCCATCTAGAACCTGGT 58.800 47.619 11.61 0.00 32.42 4.00
5163 5323 0.179089 CCAGGTCGGCAGAGAAGATG 60.179 60.000 0.00 0.00 0.00 2.90
5291 5458 2.041405 CCCTGTCCTCCCTCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
5300 5467 1.484038 CTCCCTCCTCCTGAGTCTTG 58.516 60.000 0.00 0.00 39.65 3.02
5421 5591 0.840288 TAGCTGCACTTTGGGAGGGA 60.840 55.000 1.02 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.540363 GGACAGCCGAAGAGAAACACA 60.540 52.381 0.00 0.00 0.00 3.72
72 73 2.154798 CTCGCCTCAACAGAACGGGA 62.155 60.000 0.00 0.00 0.00 5.14
75 76 0.946221 AAGCTCGCCTCAACAGAACG 60.946 55.000 0.00 0.00 0.00 3.95
93 94 0.608640 GAAGAGACCAAGAGCCCGAA 59.391 55.000 0.00 0.00 0.00 4.30
110 111 3.011566 TGAGCAAAGGTGAACCAAGAA 57.988 42.857 1.62 0.00 38.89 2.52
180 181 3.474570 GACTGGGAGCTCCGCCAT 61.475 66.667 26.36 11.76 38.76 4.40
216 217 1.896220 TCCACAATCAACTGAGTGCC 58.104 50.000 7.05 0.00 43.21 5.01
218 219 3.144506 AGCTTCCACAATCAACTGAGTG 58.855 45.455 5.65 5.65 44.76 3.51
219 220 3.406764 GAGCTTCCACAATCAACTGAGT 58.593 45.455 0.00 0.00 0.00 3.41
220 221 2.746362 GGAGCTTCCACAATCAACTGAG 59.254 50.000 0.00 0.00 36.28 3.35
221 222 2.373169 AGGAGCTTCCACAATCAACTGA 59.627 45.455 5.21 0.00 39.61 3.41
222 223 2.746362 GAGGAGCTTCCACAATCAACTG 59.254 50.000 5.21 0.00 39.61 3.16
223 224 2.641815 AGAGGAGCTTCCACAATCAACT 59.358 45.455 5.21 0.00 39.61 3.16
288 290 7.766278 CACAATACCAAGACTCTACAAATAGCT 59.234 37.037 0.00 0.00 0.00 3.32
292 294 7.770897 GGATCACAATACCAAGACTCTACAAAT 59.229 37.037 0.00 0.00 0.00 2.32
339 341 2.166664 CAGACTAACAGGACCAGGTAGC 59.833 54.545 8.81 2.70 0.00 3.58
340 342 2.166664 GCAGACTAACAGGACCAGGTAG 59.833 54.545 7.40 7.40 0.00 3.18
341 343 2.176889 GCAGACTAACAGGACCAGGTA 58.823 52.381 0.00 0.00 0.00 3.08
342 344 0.977395 GCAGACTAACAGGACCAGGT 59.023 55.000 0.00 0.00 0.00 4.00
358 360 3.677002 GGCAAGACCTAGCTAGCAG 57.323 57.895 18.83 11.93 34.51 4.24
426 428 4.882842 AAAACCGAGCCAAAAACCATAT 57.117 36.364 0.00 0.00 0.00 1.78
428 430 3.552132 AAAAACCGAGCCAAAAACCAT 57.448 38.095 0.00 0.00 0.00 3.55
457 461 4.677832 CGAAAACCTTAACAAATTGACCCG 59.322 41.667 0.00 0.00 0.00 5.28
595 601 6.768381 AGCTATTTTTACCCACTTAGAGCATC 59.232 38.462 0.00 0.00 0.00 3.91
596 602 6.663734 AGCTATTTTTACCCACTTAGAGCAT 58.336 36.000 0.00 0.00 0.00 3.79
597 603 6.062258 AGCTATTTTTACCCACTTAGAGCA 57.938 37.500 0.00 0.00 0.00 4.26
598 604 6.598064 TCAAGCTATTTTTACCCACTTAGAGC 59.402 38.462 0.00 0.00 0.00 4.09
599 605 8.561738 TTCAAGCTATTTTTACCCACTTAGAG 57.438 34.615 0.00 0.00 0.00 2.43
600 606 8.380099 TCTTCAAGCTATTTTTACCCACTTAGA 58.620 33.333 0.00 0.00 0.00 2.10
601 607 8.561738 TCTTCAAGCTATTTTTACCCACTTAG 57.438 34.615 0.00 0.00 0.00 2.18
602 608 8.161425 ACTCTTCAAGCTATTTTTACCCACTTA 58.839 33.333 0.00 0.00 0.00 2.24
603 609 7.004691 ACTCTTCAAGCTATTTTTACCCACTT 58.995 34.615 0.00 0.00 0.00 3.16
604 610 6.543735 ACTCTTCAAGCTATTTTTACCCACT 58.456 36.000 0.00 0.00 0.00 4.00
605 611 6.819397 ACTCTTCAAGCTATTTTTACCCAC 57.181 37.500 0.00 0.00 0.00 4.61
615 621 7.256154 GGGCTCTCTTTATACTCTTCAAGCTAT 60.256 40.741 0.00 0.00 0.00 2.97
617 623 5.163353 GGGCTCTCTTTATACTCTTCAAGCT 60.163 44.000 0.00 0.00 0.00 3.74
619 625 5.163499 ACGGGCTCTCTTTATACTCTTCAAG 60.163 44.000 0.00 0.00 0.00 3.02
622 628 4.500035 CCACGGGCTCTCTTTATACTCTTC 60.500 50.000 0.00 0.00 0.00 2.87
623 629 3.385111 CCACGGGCTCTCTTTATACTCTT 59.615 47.826 0.00 0.00 0.00 2.85
624 630 2.959707 CCACGGGCTCTCTTTATACTCT 59.040 50.000 0.00 0.00 0.00 3.24
637 643 1.749286 CGAATAATTTCCCCACGGGCT 60.749 52.381 0.00 0.00 43.94 5.19
638 644 0.666374 CGAATAATTTCCCCACGGGC 59.334 55.000 0.00 0.00 43.94 6.13
640 646 4.336993 TCATTTCGAATAATTTCCCCACGG 59.663 41.667 0.00 0.00 0.00 4.94
641 647 5.493133 TCATTTCGAATAATTTCCCCACG 57.507 39.130 0.00 0.00 0.00 4.94
643 649 4.952957 TGCTCATTTCGAATAATTTCCCCA 59.047 37.500 0.00 0.00 0.00 4.96
666 672 2.498078 GTCCGGTCTCCTCAAAGAGAAT 59.502 50.000 0.00 0.00 44.32 2.40
670 676 1.938585 ATGTCCGGTCTCCTCAAAGA 58.061 50.000 0.00 0.00 0.00 2.52
671 677 2.744202 CAAATGTCCGGTCTCCTCAAAG 59.256 50.000 0.00 0.00 0.00 2.77
672 678 2.105821 ACAAATGTCCGGTCTCCTCAAA 59.894 45.455 0.00 0.00 0.00 2.69
673 679 1.697432 ACAAATGTCCGGTCTCCTCAA 59.303 47.619 0.00 0.00 0.00 3.02
674 680 1.348064 ACAAATGTCCGGTCTCCTCA 58.652 50.000 0.00 0.00 0.00 3.86
683 689 2.020836 GAGGCGCGTACAAATGTCCG 62.021 60.000 8.43 0.00 0.00 4.79
684 690 1.017177 TGAGGCGCGTACAAATGTCC 61.017 55.000 8.43 0.00 0.00 4.02
687 693 0.739462 TCCTGAGGCGCGTACAAATG 60.739 55.000 8.43 0.00 0.00 2.32
698 704 0.250513 ACAAGATCCGTTCCTGAGGC 59.749 55.000 0.00 0.00 0.00 4.70
711 717 6.088824 GCATCGAAGATGAAACAAACAAGAT 58.911 36.000 13.56 0.00 45.12 2.40
719 725 1.368641 CCGGCATCGAAGATGAAACA 58.631 50.000 13.56 0.00 45.12 2.83
751 757 1.593209 GTTTGGACGTGTCAGGCGA 60.593 57.895 0.00 0.00 0.00 5.54
781 787 1.533625 TCTTCTTTGATGCCGTTGGG 58.466 50.000 0.00 0.00 0.00 4.12
791 797 3.053245 TGGTTTGGACCCTTCTTCTTTGA 60.053 43.478 0.00 0.00 45.92 2.69
843 849 2.031069 TGCAGTTGAGTCGAGTGAGTAC 60.031 50.000 18.02 2.16 0.00 2.73
845 851 1.032794 TGCAGTTGAGTCGAGTGAGT 58.967 50.000 18.02 0.00 0.00 3.41
846 852 1.413382 GTGCAGTTGAGTCGAGTGAG 58.587 55.000 18.02 0.00 0.00 3.51
847 853 0.032130 GGTGCAGTTGAGTCGAGTGA 59.968 55.000 18.02 2.08 0.00 3.41
848 854 0.946221 GGGTGCAGTTGAGTCGAGTG 60.946 60.000 10.50 10.50 0.00 3.51
856 862 1.301716 GCTTCTCGGGTGCAGTTGA 60.302 57.895 0.00 0.00 0.00 3.18
857 863 1.165907 TTGCTTCTCGGGTGCAGTTG 61.166 55.000 5.95 0.00 38.01 3.16
868 874 2.694760 CCTTGGCCGCTTGCTTCTC 61.695 63.158 0.00 0.00 40.92 2.87
871 877 4.284550 TCCCTTGGCCGCTTGCTT 62.285 61.111 0.00 0.00 40.92 3.91
872 878 4.729918 CTCCCTTGGCCGCTTGCT 62.730 66.667 0.00 0.00 40.92 3.91
923 931 2.433868 TGGCGTTGAGTACTTGAGAC 57.566 50.000 0.00 0.00 0.00 3.36
946 962 9.962783 GTAGTACACGTGAGGATTTTATCTTAT 57.037 33.333 25.01 0.00 0.00 1.73
947 963 8.959548 TGTAGTACACGTGAGGATTTTATCTTA 58.040 33.333 25.01 0.00 0.00 2.10
948 964 7.833786 TGTAGTACACGTGAGGATTTTATCTT 58.166 34.615 25.01 0.00 0.00 2.40
949 965 7.400599 TGTAGTACACGTGAGGATTTTATCT 57.599 36.000 25.01 5.26 0.00 1.98
981 997 2.370189 CCCAAGGGATAGAGGTGATCAC 59.630 54.545 17.91 17.91 37.50 3.06
1095 1129 7.980099 TCAAAAGCTATAAACTACTAGCACTCC 59.020 37.037 4.57 0.00 42.25 3.85
1103 1137 7.557724 GGAGGAGTCAAAAGCTATAAACTACT 58.442 38.462 4.18 4.18 30.65 2.57
1207 1242 1.614824 AAGGGGGAGGAGAGCACAG 60.615 63.158 0.00 0.00 0.00 3.66
1224 1262 3.843619 TCTCTCTCTCTCTCTCACTGGAA 59.156 47.826 0.00 0.00 0.00 3.53
1225 1263 3.449918 TCTCTCTCTCTCTCTCACTGGA 58.550 50.000 0.00 0.00 0.00 3.86
1227 1265 4.403752 TCTCTCTCTCTCTCTCTCTCACTG 59.596 50.000 0.00 0.00 0.00 3.66
1230 1268 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
1231 1269 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1232 1270 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1233 1271 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1234 1272 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1235 1273 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1236 1274 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1237 1275 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1238 1276 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1239 1277 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1240 1278 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1241 1279 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1242 1280 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1243 1281 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1244 1282 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1245 1283 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1246 1284 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1247 1285 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1248 1286 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1249 1287 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1250 1288 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1251 1289 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1252 1290 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1253 1291 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1254 1292 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1255 1293 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1256 1294 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1257 1295 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1258 1296 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1259 1297 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
1260 1298 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
1261 1299 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
1262 1300 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
1276 1314 5.012046 TCTCGATCTCTATCTTCTGCTCTCT 59.988 44.000 0.00 0.00 0.00 3.10
1361 1403 2.698763 GCAGCAGCAAGAAGAGGCC 61.699 63.158 0.00 0.00 41.58 5.19
1542 1602 0.453390 GAAAGGAGAAATGCAGGCCG 59.547 55.000 0.00 0.00 0.00 6.13
1580 1652 2.214292 GCAACAACGCACACACACG 61.214 57.895 0.00 0.00 0.00 4.49
1618 1690 7.846066 AGAACTCTGAACTTGCTAGATGTTAT 58.154 34.615 1.04 0.00 0.00 1.89
1619 1691 7.233389 AGAACTCTGAACTTGCTAGATGTTA 57.767 36.000 1.04 0.00 0.00 2.41
1642 1714 9.443283 CAATCTAAATTAAATTCGCAGAGGAAG 57.557 33.333 0.00 0.00 38.43 3.46
1663 1736 2.211250 ATGCAGCACAGTTCCAATCT 57.789 45.000 0.00 0.00 0.00 2.40
1676 1749 3.397482 ACAAAGATCCGAGATATGCAGC 58.603 45.455 0.00 0.00 0.00 5.25
1704 1777 7.214821 TCGTAATTCGTTGATATTTGCGAAAAC 59.785 33.333 11.26 11.16 44.61 2.43
1707 1780 6.333839 TCGTAATTCGTTGATATTTGCGAA 57.666 33.333 10.15 10.15 45.32 4.70
1737 1810 3.200958 TCCCCAGGTAGAAAACTAGCT 57.799 47.619 0.00 0.00 38.06 3.32
1739 1812 6.722328 AGAAATTCCCCAGGTAGAAAACTAG 58.278 40.000 0.00 0.00 0.00 2.57
1762 1843 4.938226 AGTCGAATAAAAGAAGGCAAGGAG 59.062 41.667 0.00 0.00 0.00 3.69
1795 1876 3.573967 TGAGATCCCAAAAGGCAGTTTTC 59.426 43.478 0.00 0.00 36.11 2.29
1875 1956 5.163663 TGGCATTAAACTCGATCCACAATTC 60.164 40.000 0.00 0.00 0.00 2.17
1880 1961 4.900635 AATGGCATTAAACTCGATCCAC 57.099 40.909 11.81 0.00 0.00 4.02
1911 1992 5.416271 AGGCAGTAGATTCTAACGGAAAA 57.584 39.130 0.00 0.00 37.49 2.29
1912 1993 5.163478 GGTAGGCAGTAGATTCTAACGGAAA 60.163 44.000 0.00 0.00 37.49 3.13
1926 2007 4.390129 TTGAATTTTGGGGTAGGCAGTA 57.610 40.909 0.00 0.00 0.00 2.74
1932 2013 7.394359 TGAAGAGAGATTTGAATTTTGGGGTAG 59.606 37.037 0.00 0.00 0.00 3.18
1934 2015 6.077322 TGAAGAGAGATTTGAATTTTGGGGT 58.923 36.000 0.00 0.00 0.00 4.95
1959 2040 2.125766 GAACGGCCCTTCCCTGAACT 62.126 60.000 0.00 0.00 0.00 3.01
2004 2089 8.541133 AGAAGATGAACAGTAGAGCTTTTTAC 57.459 34.615 0.00 0.00 0.00 2.01
2087 2178 0.533755 ACTGCAACACACAGAGGAGC 60.534 55.000 0.00 0.00 38.55 4.70
2180 2271 2.503356 AGGTGGTGAGGAAGATCATGAC 59.497 50.000 0.00 0.00 0.00 3.06
2336 2436 6.326375 TGAACAATGTAACAAGTTGGTGAAC 58.674 36.000 2.90 0.00 0.00 3.18
2338 2438 5.883115 TCTGAACAATGTAACAAGTTGGTGA 59.117 36.000 2.90 0.00 0.00 4.02
2516 2619 1.352156 CCTTGTAGACGCAGCCGAAC 61.352 60.000 0.00 0.00 38.29 3.95
2587 2690 3.764466 CCTTCTCGCAGTCCGGCT 61.764 66.667 0.00 0.00 37.59 5.52
2606 2709 2.737252 GGAGTCAACATTCACCTCGAAC 59.263 50.000 0.00 0.00 36.12 3.95
2668 2771 7.546358 CATTTTACATTCATAGCAAGAACCCA 58.454 34.615 0.00 0.00 0.00 4.51
2669 2772 6.476706 GCATTTTACATTCATAGCAAGAACCC 59.523 38.462 0.00 0.00 0.00 4.11
2680 2783 5.636121 CACAGCACAAGCATTTTACATTCAT 59.364 36.000 0.00 0.00 45.49 2.57
3055 3160 3.274288 GAAAAATCATCACTCGGGCTCT 58.726 45.455 0.00 0.00 0.00 4.09
3065 3170 5.177142 CGGCACAACAATTGAAAAATCATCA 59.823 36.000 13.59 0.00 0.00 3.07
3116 3222 8.254508 GCCCAGTTTCAATTTACCAATGTTATA 58.745 33.333 0.00 0.00 0.00 0.98
3117 3223 7.102993 GCCCAGTTTCAATTTACCAATGTTAT 58.897 34.615 0.00 0.00 0.00 1.89
3118 3224 6.042093 TGCCCAGTTTCAATTTACCAATGTTA 59.958 34.615 0.00 0.00 0.00 2.41
3119 3225 5.163258 TGCCCAGTTTCAATTTACCAATGTT 60.163 36.000 0.00 0.00 0.00 2.71
3120 3226 4.346418 TGCCCAGTTTCAATTTACCAATGT 59.654 37.500 0.00 0.00 0.00 2.71
3121 3227 4.892433 TGCCCAGTTTCAATTTACCAATG 58.108 39.130 0.00 0.00 0.00 2.82
3122 3228 4.020307 CCTGCCCAGTTTCAATTTACCAAT 60.020 41.667 0.00 0.00 0.00 3.16
3123 3229 3.323403 CCTGCCCAGTTTCAATTTACCAA 59.677 43.478 0.00 0.00 0.00 3.67
3124 3230 2.896685 CCTGCCCAGTTTCAATTTACCA 59.103 45.455 0.00 0.00 0.00 3.25
3125 3231 2.233676 CCCTGCCCAGTTTCAATTTACC 59.766 50.000 0.00 0.00 0.00 2.85
3280 3386 5.334879 GGTTACCTGCAGTCAACATGTAAAG 60.335 44.000 22.14 3.75 32.39 1.85
3498 3606 7.712205 AGAATTTTGCTGCTCACAGTTTATTTT 59.288 29.630 0.00 0.00 46.30 1.82
3499 3607 7.212274 AGAATTTTGCTGCTCACAGTTTATTT 58.788 30.769 0.00 0.00 46.30 1.40
3508 3616 3.930634 AAGGAGAATTTTGCTGCTCAC 57.069 42.857 0.00 0.00 32.56 3.51
3512 3620 4.813027 TGATGAAAGGAGAATTTTGCTGC 58.187 39.130 0.00 0.00 0.00 5.25
3736 3849 3.844577 AGCTGACTGATCAAATTGTGC 57.155 42.857 0.00 0.00 33.30 4.57
3751 3864 7.176490 AGAGAACTAGTTACTTCCTAAGCTGA 58.824 38.462 8.42 0.00 0.00 4.26
3752 3865 7.399245 AGAGAACTAGTTACTTCCTAAGCTG 57.601 40.000 8.42 0.00 0.00 4.24
3789 3902 5.464168 AGAATGCTATGTTGCAACAGAAAC 58.536 37.500 33.44 24.07 46.61 2.78
4018 4131 2.012673 GGCATAGAGAACAACAGCCTG 58.987 52.381 0.00 0.00 37.67 4.85
4147 4260 0.543410 TAACTCTGAGCGTTCCCCCA 60.543 55.000 4.19 0.00 0.00 4.96
4237 4350 4.042174 TGGACCGTATAATTCCCTTTCCT 58.958 43.478 0.00 0.00 0.00 3.36
4294 4408 0.902531 GTAAGCAGCAGGGACAGGTA 59.097 55.000 0.00 0.00 0.00 3.08
4313 4427 0.754957 AGCTCTCACTCATCCTCGGG 60.755 60.000 0.00 0.00 0.00 5.14
4315 4429 0.667993 GGAGCTCTCACTCATCCTCG 59.332 60.000 14.64 0.00 38.50 4.63
4440 4558 1.002430 GCAGTGACCAGATCCACAGAA 59.998 52.381 0.00 0.00 35.84 3.02
4542 4660 2.128771 ACAGAACTGTTGCCAACTGT 57.871 45.000 13.57 13.57 41.83 3.55
4592 4720 2.390288 CGTTGCGATCGTTGTCCG 59.610 61.111 17.81 8.49 38.13 4.79
4593 4721 1.897398 AAGCGTTGCGATCGTTGTCC 61.897 55.000 17.81 0.00 0.00 4.02
4598 4727 1.805945 GAGGAAGCGTTGCGATCGT 60.806 57.895 17.81 0.00 0.00 3.73
4620 4749 8.471457 CACGTGCTGCATTATATTTATGTTTTC 58.529 33.333 5.27 0.00 0.00 2.29
4643 4772 4.330894 CCTGCCTATATGAATATGTGCACG 59.669 45.833 13.13 0.00 31.66 5.34
4660 4789 9.827198 TGATTATTATCATTATTTTCCCTGCCT 57.173 29.630 0.00 0.00 35.87 4.75
4661 4790 9.860898 GTGATTATTATCATTATTTTCCCTGCC 57.139 33.333 0.00 0.00 42.49 4.85
4701 4840 7.884257 TCATGTTCATGCTCAGTCAATTTAAA 58.116 30.769 7.80 0.00 0.00 1.52
4715 4854 5.461078 GGCTGATTTATGTTCATGTTCATGC 59.539 40.000 7.80 8.06 0.00 4.06
4731 4870 8.199449 CCTTGTGAAATTATACATGGCTGATTT 58.801 33.333 11.51 0.00 35.97 2.17
4734 4873 6.422333 TCCTTGTGAAATTATACATGGCTGA 58.578 36.000 16.14 3.87 40.20 4.26
4759 4898 7.654568 CATGCTCAAAACATATATGGACATGT 58.345 34.615 16.96 0.00 36.96 3.21
4908 5053 2.024655 ACCTTGATTGCCCATGATGTCT 60.025 45.455 0.00 0.00 0.00 3.41
4958 5108 0.984230 TTACTTGACTGCCCTGGGAG 59.016 55.000 19.27 13.41 39.56 4.30
4985 5135 7.976135 TGGCATGTAAAGCAAATTTTTATGT 57.024 28.000 0.00 0.00 31.12 2.29
4989 5139 8.313292 TCTAGATGGCATGTAAAGCAAATTTTT 58.687 29.630 3.81 0.00 32.01 1.94
5021 5174 0.813821 GGAGGGCATCAGAAGCAAAC 59.186 55.000 0.08 0.00 0.00 2.93
5022 5175 0.700564 AGGAGGGCATCAGAAGCAAA 59.299 50.000 0.08 0.00 0.00 3.68
5079 5232 6.095300 TGCAAGTTTTTGTCTCTGAATTCTGA 59.905 34.615 13.64 13.64 36.65 3.27
5163 5323 2.289010 CCCCATCAAGCAAGGAAAACAC 60.289 50.000 0.00 0.00 0.00 3.32
5291 5458 5.634859 AGCAAAACAAAAACACAAGACTCAG 59.365 36.000 0.00 0.00 0.00 3.35
5300 5467 7.020602 ACAGCAAATAAGCAAAACAAAAACAC 58.979 30.769 0.00 0.00 36.85 3.32
5392 5562 0.947244 AGTGCAGCTACAGCAACAAC 59.053 50.000 3.70 0.00 44.64 3.32


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.